Automated Slide Processing Systems, Consumable Stainer Units, and Related Technologies

This application is a continuation of U.S. patent application Ser. No. 17/151,053, filed Jan. 15, 2021, which is a continuation of PCT Application No. PCT/EP2019/068809, filed Jul. 12, 2019, which claims priority to U.S. Provisional Application No. 62/698,802, filed Jul. 16, 2018, which are hereby incorporated by reference in their entireties.

This disclosure relates to systems for preparing samples for analysis. In particular, the disclosure relates to automated slide processing systems, consumable stainer units, and related technologies for processing samples.

A wide variety of techniques have been developed to prepare and analyze biological specimens. Example techniques include microscopy, microarray analyses (e.g., protein and nucleic acid microarray analyses), and mass spectrometric methods. Specimens are typically prepared for analysis by applying one or more liquids (e.g., reagents) to the specimens. If a specimen is treated with multiple liquids, both the application and subsequent removal of each liquid can be important for producing stained specimens suitable for analysis. For example, microscope slides bearing biological specimens, e.g., tissue sections or cells, are often treated with a series of manually applied reagents to add color and contrast to otherwise transparent or invisible cells or cell components. This labor-intensive process often results in inconsistent processing due to individual techniques among laboratory technicians.

Automated slide processing machines are often used for high-volume slide processing. Unfortunately, conventional automated slide processing machines are typically relatively large, thus making them unsuitable for use in surgery suites and small laboratories. For example, conventional automated pipetting systems can be quite large and have pipetting heads capable of individually dispensing liquids onto specimen-bearing microscope slides held by a tray. Pipettes are used to aspirate reagents out of bottles and to dispense the reagents onto uncovered slides. The reagents are exposed to air which can lead to degradation, e.g., due to oxidation, or biologic contamination of solution components over time. This can lead to inconsistent staining unless the solutions are regularly replenished or exchanged. Replenishing or exchanging liquids can be a time-consuming and wasteful process that often disrupts work-flow. Additionally, automated pipetting systems have a limited number of reagent bottles, thus limiting the number of staining protocols that can be performed or necessitating swapping which negatively impacts workflow. Accordingly, conventional automated slide processing machines suffer various drawbacks.

At least some embodiments include a staining system for preparing and analyzing biological specimens. The staining system can include a consumable stainer unit for processing microscope slides bearing biological specimens with a series of automatically applied reagents to add color stains and background contrast to otherwise transparent or invisible cells or cell components. The stainer unit can include reagent dispensing elements, a slide processing station which can control temperature, reagent removal elements, and sealed reagent holders with reagents. The stainer unit can be integrated into an instrument in a laboratory environment. In some embodiments, the stainer unit can also include containers to capture used and unused reagents for safe and convenient disposal. The stainer unit can contain the specimen slide and can prevent, limit, or minimize evaporative losses, stain degradation (e.g., due to oxidation), and minimize or eliminate the possibility of tissue cross-contamination, or other problems. Accordingly, the stainer unit can be used to control reagent characteristics (e.g., concentrations, mixtures, etc.) to enhance the effectiveness of the reagents, resulting in desired staining characteristics. In single use embodiments, the stainer unit can have enough reagent to perform a single multistep staining protocol to avoid reagent waste and can be made of relative low-cost materials. To process multiple slides, each slide can be processed with a consumable stainer unit selected from a family of consumables based on the reagents stored within them, and the staining protocol required. Manual procedures, automated procedures, or combination of manual and automated procedures can be used to process the slides.

Aspects of the technology are directed, for example, to an automated staining system having an instrument with at least one end effector and a stainer unit-receiving station. The instrument causes reagent to be delivered to the flow cell of the consumable stainer unit. The consumable stainer unit can carry fresh reagents, waste material, and components used to handle the reagents. In some embodiments, most of the fresh reagent is delivered to the flow cell to process the specimen. During processing, multiple aliquots of reagent can be delivered from the same reagent reservoir to the flow cell. All or some of the reagents contained in the consumable stainer unit may be captured in a waste container integrated into the consumable stainer unit upon completion of the specimen processing operations. For example, at least 50%, 60%, 70%, 80%, 90%, and 95% of the total volume of reagent, including fresh and used reagent, carried by the consumable stainer unit can be contained in the waste container. The waste container can include a means to allow the egress of air (e.g., to prevent back-pressure developing) and to ensure that substantially no used reagent liquid escapes from the reservoir.

In some embodiments, a staining system can include a slide processing cartridge having a flow cell, reagent reservoirs, and a waste container fluidly coupled to the flow cell. The flow cell has a slide-receiving region and a sealing ring. The slide-receiving region is dimensioned to receive a microscope slide such that the sealing ring sealingly contacts a specimen-bearing surface of the microscope slide to define a reaction chamber along the specimen-bearing surface. Reagent can be sequentially delivered from the reagent reservoirs to the flow cell in order to perform a set of slide tissue processing operations. In automated procedures, the staining system can include an instrument with an end effector and a cartridge-receiving station. The end effector is capable of engaging a dispenser of the slide processing cartridge, which is positioned at the cartridge-receiving station, in order to cause reagent to be delivered from a respective one of the reagent reservoirs to the flow cell. The instrument can be configured to use the slide processing cartridge to perform a staining protocol without contacting the reagents to reduce the frequency of instrument maintenance. In manual procedures, a user can manually operate dispensers of the slide processing cartridge. The actuators can have predetermined volumes of reagents to simplify manual operation.

The slide processing cartridge can be configured to sequentially delivery reagents from the closed reagent reservoirs to the flow cell for fluid exchange cycles and to cause the reagents to flow from the flow cell to the waste reservoir. The dispenser can be a pipette, a blister element, or a syringe element and can, for example, employ electrical actuation and/or pneumatics to provide motive forces. The specimen slide processing cartridge can include a base (e.g., a planar platform) with a fluid circuit that fluidly couples the dispensing element(s) to the flow cell and that fluidly couples the flow cell to the waste container. The fluid circuit can include one or more fluid passageways, fluid lines, valves, air-trap features, or the like.

The flow cell has an inlet region a specimen containing flow cell region and an outlet region. The inlet region can widen laterally in a downstream direction to allow liquid reagent to spread outwardly into the flow cell with minimal turbulent flow. The reaction chamber can have a substantially polygonal shape (e.g., substantially hexagonal shape or substantially rectangular shape), elliptical shape, or the like.

In some embodiments, a stainer unit for processing slides includes a support base and a flow cell connected to the support base. The flow cell can include a slide engagement region having a surface and a sealing member. The sealing member is configured to sealingly contact a specimen-bearing surface of a microscope slide to define a flow cell between the surface of the slide engagement region and the specimen-bearing surface. In some embodiments, the reaction chamber/flow cell can be sealed by one or more valves positioned along entry and exit fluid lines or passageways, and the sealing arrangement provided via the reaction chamber seals. Reagents can be held in the reaction chamber to maintain hydration of the specimen and provide a suitable target with associated marker, e.g., antibody, DNA probe, dye molecule, or the like. The stainer unit, including the sealed reaction chamber, can then be heated to temperatures higher than the boiling temperature of the reagent (e.g., a primarily water based reagent) to provide enhanced antigen retrieval or other types of processing. The flow cell area can be provided with suitable physical support on upper and lower surfaces to ensure seals are maintained even when high pressure is experienced. Such high pressures can inhibit or prevent boiling when the reagent is at temperatures equal to or higher than 100° C., 105° C., 110° C., 120° C. or 130° C. such that enhanced staining can be achieved in very short periods of time. Fresh reagent can be pumped through an open inlet valve and into the reaction chamber while used reagent is pushed through an open outlet valve. The inlet and outlet valves can be closed again to perform additional high temperature steps.

The stainer unit can also include a plurality of reagent reservoirs, which are supported by the base, and at least one dispenser. The dispenser can be configured to deliver reagent from each of the reagent reservoirs to a flow cell.

The dispenser can establish fluid communication with the flow cell to perform a staining protocol in which the microfluidic microscope slide processing cartridge contains all the reagents needed to support the staining protocol. The dispenser can include one or more pipette tips, blister elements holding reagents, sealed reagent containers, and/or actuators holding reagents. The dispenser can be coupled to or integrated with the support base. In some embodiments, reagent packs can be physically separated from the rest of the microscope slide processing cartridge.

A waste container can be supported by the base and fluidically coupled to the flow cell. The waste container receives and contains reagent from the flow chamber. In some embodiments, the waste container is detachably coupled to the support base. The waste container is sealed to hold waste reagent after it has been detached from the support base. The stainer unit can include a one-way valve that allows waste reagent to flow into the waste container, and to prevent any backflow of used reagent. The waste container can be detached from the support base while the microscope slide is positioned at the slide engagement region. In some embodiments, the waste container includes an air-egress element (e.g., a valve) that allows the egress of air to prevent or limit back-pressure and inhibits or prevents used reagent liquid from escaping from the waste container.

In some blister element embodiments, the dispensers are in the form of a first blister actuator operable to dispense a first reagent from a first one of the reagent reservoirs, a second blister actuator operable to dispense a second reagent from a second one of the reagent reservoirs, and a third actuator operable to cause a rinse solution to flow into the flow chamber. A fluid circuit can fluidly couple each of the blisters to the flow cell, and the fluid circuit can include fluid passageways in the base.

In some embodiments, the reagent reservoirs can contain reagent-filled pouches. Plungers are movable to cause a respective one of the reagent-filled pouches to release reagent. The plungers can burst the reagent-filled pouches.

In yet further embodiments, a stainer unit includes regents and a reaction cell configured to at least partially define a reaction chamber. The stainer unit can include a fluid circuit that allows the reagents to be delivered to the reaction chamber. The fluid circuit can seal the reaction cell to inhibit or prevent evaporation and/or boiling of one or more of the reagents in the reaction chamber during, for example, high-temperature processing. The fluid circuit can include one or more valves in fluid communication with the reaction chamber. The valves can be located along passageways in fluid communication with the reaction chamber. In some embodiments, the fluid circuit allows the regents to be sequentially delivered to the reaction chamber and inhibits or prevents fluid flow away from reaction chamber. The sealed reaction cell can increase a boiling point of the reagent to accelerate high-temperature antigen retrieval. The reaction chamber can be located along a specimen-bearing surface of a microscope slide or at another suitable location, and the reaction cell can be a flow cell through which reagents can flow and be held in contact with the specimen.

In further embodiments, a method includes performing a plurality of specimen processing operations on a specimen held in a flow cell at least partially defined by a mounting surface of a slide carrying the specimen. The processing can include sequentially delivering reagents from two or more reservoirs of a microscope slide cartridge to a reaction chamber of the flow cell. The used reagent can be delivered into a waste container fluidly coupled to the flow cell.

The microscope slide cartridge can carry the microscope slide while the microscope slide cartridge is removed from and/or delivered to an automated instrument. Each reagent can be delivered through a fluid circuit of the microscope slide cartridge to deliver reagent into the reaction chamber and to deliver waste reagent to waste container.

In further embodiments, a method includes processing a plurality of specimens within the same cartridge. The processing can include applying the same reagents to multiple specimens either simultaneously or sequentially.

The method can include sequentially delivering a first reagent from the first reservoir to the reaction chamber, delivering a wash liquid to the reaction chamber, and delivering a second reagent from the second reservoir to the reaction chamber. The wash liquid can remove most of the first reagent by volume from the reaction chamber prior to delivery of the second reagent. Additional alternating wash and reagent cycles can be performed.

The microscope slide cartridge can be delivered to an automated instrument while the microscope slide cartridge carries most of the reagents that are used in specimen processing operations. After performing specimen processing operations, the microscope slide cartridge can be removed from the automated instrument. The waste container can be separated from a base of the microscope slide cartridge by the user or the instrument for disposal.

In some embodiments, a significant portion or most of the reagent in one or more of the reservoirs (e.g., all of the reservoirs) is delivered to the flow cell to process the specimen. During processing, multiple aliquots of reagent can be delivered from the same reservoir to the flow cell. Most of the reagent contained in the microscope slide cartridge can be carried in the waste container upon completion of specimen processing operations. For example, most of the reagent, by weight, can be carried by the waste container. For example, at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 95% of the total volume of reagent carried by the microscope slide cartridge is contained in the waste container.

The following description of several embodiments describes non-limiting examples of the disclosed system and methods to illustrate the technology. Furthermore, all titles and headings provided herein are for convenience only and are not intended to limit or interpret the scope or meaning of the invention. Specific details of several embodiments of the present technology are disclosed herein with reference to. In the figures, the same reference numerals refer to like parts or acts throughout the various views, unless otherwise specified. It should be noted that other embodiments in addition to those disclosed herein are within the scope of the present technology. For example, embodiments of the present technology can have different configurations, components, substances, and/or procedures than those shown or described herein. Moreover, a person of ordinary skill in the art will understand that embodiments of the present technology can have configurations, components, substances, and/or procedures in addition to those shown or described herein and that these and other embodiments can be without several of the configurations, components, and/or procedures shown or described herein without deviating from the present technology.

is a front view of an automated specimen processing system(“system”) in accordance with an embodiment of the disclosed technology. The systemcan include a robotic staining instrumentand consumable stainer units,. The staining instrumentcan include a protective housing, a loading zone or station(“station”), and a controller. The stationcan include a door or access portfor loading and unloading stainer units,, illustrated schematically, carrying specimen-bearing microscope slides. Each stainer unit,can contain sealed reagent reservoirs and a waste container. The staining instrumentcan use the reagents on-board the unitsto process the specimens. After processing, the stainer units,can be retrieved from the instrument, the specimen-bearing slides can be removed from the stainer units,, and the specimens can be analyzed. The system can be provided with storage capability, for example a stainer unit holding rack from which the system can access stainer units to be processed, and capable of re-inserting stainer units at various stages of assay completion.

Each stainer unit,(collectively “stainer units”) can contain most or all of the substances for performing the assay, for example, specimen conditioning (e.g., cell conditioning, washing, etc.), antigen/target retrieval, staining (e.g., hematoxylin and eosin staining), or other types of protocols (e.g., immunohistochemistry protocols, in situ hybridization protocols, etc.) for preparing specimens for visual inspection, fluorescent visualization, microscopy, microanalyses, mass spectrometric methods, imaging (e.g., digital imaging), or other analytical or imaging methods. The fluids can be held in airtight containers to minimize or limit the possibility of reagent oxidation that could impact staining even when the stainer unit is stored for relatively long periods of time (e.g., months or years). The single doses also limit thermal exposure to other stored reagents when taken out of temperature controlled environments (e.g., when removed from a refrigerator). The stainer unitscan include a reaction chamber and fluid lines, channels, valves, ports, pressurization devices (e.g., pumps, syringes, etc.), or other components for fluidly communicating with the reaction chamber. The stainer unitscan also include one or more mixing components (e.g., mixing wells, reagent trays, etc.) for mixing reagents in, for example, lyophilized and/or liquid form. The configuration of the stainer unit and onboard substances can be selected based upon the staining protocol to be performed and functionality of the staining instrument.

Multiple stainer units can be available to perform different protocols. For example, the stainer unitcan have reagents for performing hematoxylin and eosin (H&E) staining and the stainer unitcan have reagents for performing advanced staining protocols, such as immunohistochemistry protocols or in situ hybridization protocols. In some single-use embodiments, each stainer unitcan carry a sufficient amount of reagent to perform only a single protocol using fresh reagents to avoid producing excess reagent waste. The reagent reservoirs and waste containers can be permanently sealed to prevent reuse. The sealed containers can also facilitate disposal. In some multi-use embodiments, the reagent reservoirs can be refilled any number of times and the reagent chamber can be flushed and washed. The stainer unitscan contain waste materials for convenient disposal. The waste materials can include waste reagents, wash solutions, or other fluids that can be collected in a removable waste container that can be discarded separately from other components of the stainer unit. This allows for separate handling of unused and used liquids.

The controllercan be used to select protocols and can receive information. The information can be inputted by the user using an input device, such as a keyboard, a touchscreen, or the like. In some embodiments, the staining instrumentincludes one or more readers in communication with the controller. The readers can obtain information from machine readable labels, barcodes, or other types of labels applied to, for example, the microscope slides, stainer units, or reagent reservoirs. The controllercan command system components based, at least in part, on the obtained information, and can generally include, without limitation, one or more processors, computers, central processing units, microprocessors, digital signal processors (DSPs), application-specific integrated circuits (ASICs), readers, or the like. In some embodiments, the controllercan be programmed to receive information from microscope slides, process specimens based on the received information, and acquire one or more images of the processed specimens.

To store information, the controllercan include, without limitation, one or more storage elements, such as memory (e.g., volatile memory, non-volatile memory, read-only memory (ROM), random access memory (RAM)). For example, the memory can be non-transitory computer-readable memory that stores instructions that, when executed by a processor, cause the controllerto perform operations. The stored information can include, without limitation, reagent information, expiration information (e.g., expiration dates), stainer unit information, staining protocols, reagent recipes, heating programs, optimization programs, calibration programs, indexing programs, databases, imaging programs, and/or executable programs. The protocols can include reagent protocols (e.g., number and/or order of reagents applied), thermal protocols (e.g., heating/cooling routines), and other executable instructions for processing slides. The stored information can be used to determine, for example, protocols for processing the stainer unit based on information acquired from the stainer unit, inputted by an operator, or both, for example. In some embodiments, the instrumentcan obtain information from the stainer unit and additional information from the microscope slide. The stainer unit information can indicate reagent volumes, staining protocol, or the like. The microscope slide information can include tissue information and staining to be performed. Based on that information, the controllercan determine an appropriate protocol for processing the tissue specimen based on the available resources, and if another stainer unit should be used, a notification can be provided to the user.

In operation, a user can manually load the stainer unitwith a specimen-bearing microscope slide. The user can visually confirm proper loading and can then feed the stainer unitto the instrument. In other embodiments, the user separately loads microscopes slides and stainer unitsinto the staining instrument, which can robotically load the stainer units with the microscope slides. Closed reagent chambers of the stainer unitscan prevent, limit, or minimize evaporative losses, stain degradation, cross-contamination between slides (typically experienced with dip and dunk systems), or other problems, thereby enabling control of reagent characteristics (e.g., concentrations, mixtures, etc.) to enhance the effectiveness of the reagents and resulting in desired staining characteristics.

The staining instrumentcan controllably dispense fresh processing liquids onto the slides without splattering onto its mechanical or electrical components, as well as adjacent slides often present in conventional pipetting systems, and can controllably remove processing liquids from the slides via vacuum or liquid replacement or other suitable means. The controlled reagent dispensing/removal reduces volumes of liquid waste (e.g., waste reagents which have passed through the reaction chamber) by, for example, minimizing or otherwise limiting volumes of utilized reagents. In some embodiments, specimen processing may include contacting specimens with a series of liquids that include, for example, one or more deparaffinizing liquids, conditioning liquids, staining reagents, stain-differentiating reagents, stain-setting reagents, washing liquids, and/or coverslipping liquids.

The stainer unitscan contain the reagents throughout processing such that the staining instrumentcan process specimens without contacting the reagents. For example, the stainer unitscan hold aliquots of reagent and can cause reagents to flow into a reaction chamber and into contact with a specimen. In some procedures, most of the reagent from multiple reservoirs is delivered to the flow cell to process the specimen. Most of the reagent, by volume, can be contained in the stainer unitsis carried in a waste container upon completion of the specimen processing operations. For example, the waste container contains most of the reagent, by weight or volume, carried by the used stainer unit. In some procedures, the waste container contains at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 95% of the total volume of reagent carried by the stainer unit. The used stainer unit, which still carries the unused reagents and waste reagent, can be removed from the instrumentfor subsequent disposal.

The stainer unitscan have integrated coverslips for viewing the specimen, thereby avoiding an additional coverslipping step. In some embodiments, the staining instrumentcan perform a coverslipping operation. After coverslipping, the stainer unit, which carries the coverslipped slide, can be retrieved at the station. In other embodiments, the microscope slide can be coverslipped after removal from the instrument. Additional processing can be performed on the slide.

is a front view of internal components of the instrumentin accordance with an embodiment of the disclosed technology. The instrumentcan include a dispenser apparatusconfigured to operate the stainer unitin the form of a microfluidic slide processing cartridge, illustrated at a cartridge-receiving station. The stainer unitcan be include a base, a reagent unit, and a flow cell. The basecan include fluid components for delivering reagents to the flow cell. The instrumentcan deliver, or cause to be delivered, reagents from reagent reservoirs of the reagent unitto the flow cell.

The flow cellcan be a microfluidic cell capable of holding small volumes of liquid. This allows all or most of the reagents, by volume or weight, to be carried onboard the stainer unit. For example, microfluidic flow cells can hold less than, for example, about 25 μL, about 50 μL, about 100 μL, about 150 μL or about 200 μL. In some embodiments, the flow cellcan hold about 25 μL to about 100 μL, about 50 μL to about 120 μL, about 75 μL to about 120 μL, or other desired volumes. The specimen and reagent can be heated to a temperature equal to or higher than about 60° C., about 70° C., about 80° C., about 90° C., about 100° C., about 110° C., or about 120° C., or other desired temperatures. In some embodiments, the instrumentoperates to apply heat to the specimen to provide a dwell temperature equal to or less than 60° C., about 70° C., about 80° C., about 90° C., about 100° C., about 110° C., or about 120° C. for a period of time. The period of time can be equal to or less than about 10 minutes, about 15 minutes, or about 20 minutes. The reagent unitcan be generally thermally isolated from the flow cellto prevent or limit excessive heating of the standby reagents when the specimen is heated to high temperatures, for example, 120° C. In some embodiments, the flow cellgenerates thermal energy to heat the specimen and/or reagents. For example, the flow cellcan include one or thermal elements (e.g., resistive heaters, Peltier devices, etc.) to generate the thermal energy.

The flow cellcan be used for deparaffinization, antigen/target retrieval, and staining using minimal volumes of fluid and can be configured for mixing (e.g., via agitation) or producing minimal diffusion layers to minimize or limit processing times. The flow cellcan contact the mounting surface of the slide to form a fluid-tight seal that is maintained throughout processing even when heat is applied to the specimen and the reagent, with a dwell at 100° C., 110° C., 120° C. for up to about 20 minutes. The liquid reagent, such as primarily water-based reagents, can be heated to temperatures higher than their normal boiling points to provide enhanced antigen/target retrieval. The flow cell area can be isolated by one or more seals (e.g., air-tight seals, fluid-tight seals, etc.) that can be maintained even when high pressures are experienced. This ensures that the reagents do not boil even at high altitude when the reagent is a temperature equal to or higher than 80° C., 90° C., 100° C., etc. The high-temperature processing enables enhanced staining in very short times. In some embodiments, the stainer units have pressurizable flow cells for high-temperature antigen/target retrieval. To raise the boiling point of the reagent, one or more valves can seal the reaction chamber by inhibiting or preventing the flow of fluid out of the reaction chamber, thereby raising a boiling point of the reagent. For example, the reaction chamber can be closed and pressurizable to raise the boiling point of the reagent (e.g., a reagent with a suitable antibody with associated marker) at least about 5%, 10%, 20%, or 30%.

The flow cellcan also remain sealed during processing to limit or prevent specimen loss, air bubble formation, or other problems, such as measurable evaporative losses. Thermal energy can be delivered uniformly or non-uniformly across the slide via conduction to produce a substantially uniform temperature profile along a specimen-bearing portion of the slide surface. In some embodiments, the substantially uniform temperature profile has a temperature variation equal to or less than a selected temperature variation across the specimen-bearing surface to achieve acceptable stain variation intensity. Non-uniform temperature profiles can also be produced along the slide or specimen if desired.

In some IHC protocols, multiple rinses at temperatures in a range between about 20° C. and about 70° C. can be applied. The rinses can include, without limitation, hydrophobic substances and organic solvents. Multiple dispense and removal steps can be performed. Each step can be performed at temperatures in a range of about 20° C. to about 70° C. and can utilize predetermined amounts of multiple reagents. The reagents can be combined prior to tissue contact. During a dwell period, the reagents within the flow cell can cover the entire specimen and, in some embodiments, can be agitated to achieve suitable staining performance. The sample can then be dehydrated and a coverslipping agent can be applied to the slide. A coverslip can be applied and the coverslipping agent can be heated to a suitable curing temperature (e.g., 70° C., 80° C., 90° C., or another suitable temperature). Alternatively, the flow cell can have an integrated coverslip. The stainer unit can allow visual access to both sides of the slides for automated imaging and visual inspection of the specimen.

The instrumentcan perform one or more washing cycles to add and subsequently wash reagents from the flow cell. After incubation, reagent can be washed from the flow cellto remove unreacted reagent that could affect a subsequent processing step. A washing cycle can include flushing the flow cellwith an excess of buffer or wash solution. The unreacted reagent can be diluted with the excess volume of the buffer or wash solution and driven out of the flow cell. In some embodiments, a washing cycle can include flushing the flow cellwith the wash solution. The wash solution could be miscible or immiscible with the prior reagent. In some embodiments, a washing cycle can include flushing the flow cell with a gas (e.g. air). In some protocols, a washing cycle can be performed for fluid exchange after each incubation.

Dispenser apparatuscan include a transporter apparatusand an end effector. The transporter apparatuscan include, without limitation, one or more rail assemblies, robotic handlers, X-Y-Z transport systems, conveyors, drive elements(e.g., actuators, drive motors, or the like), or other automated mechanisms or components. In some embodiments, the dispenser apparatuscan include a plurality of pumps, compressors, vacuum devices (e.g., blowers), and/or other devices capable of pressurizing fluids and/or providing a vacuum (including a partial vacuum). To perform multi-step protocols, the end effectorcan sequentially deliver reagents from reagent reservoirs to a reaction chamber of the flow cell. The end effectorcan include, without limitation, one or more orifices (e.g., jewel orifices), ports, nozzles, valves (e.g., one-way valves, check valves, pressure relief valves, etc.), sensors (e.g., pressure sensors, fluid detection sensors, etc.), grippers, pipette holders, pressurization devices (e.g., pumps), or other components for operating stainer units, controlling liquid delivery, or the like. The configuration and functionality of the end effectorcan be selected based on the configuration of the stainer unit.

The stainer unitcan include a closure device(e.g., a clamp) that applies pressure to the microscope slide, flow cell, etc. For example, the closure devicecan apply sufficient pressure to a backside of a microscope slide to maintain a seal at the front side of a downwardly facing slide. By way of another example, the closure devicecan apply pressure to a cover overlying the front side of an upwardly facing slide. The slide can be a generally rectangular piece of a transparent material having a front side or face for receiving the specimen. The slide can have a length of about 75 mm (3 inches), a width of about 25 mm (1 inch), and a thickness of about 1 mm (0.04 inch) and, in certain embodiments, may include a label and such a label can include characters and/or other machine-readable codes such as a barcode or an RFID tag. In other embodiments, information can be etched into the microscope slide or included within the microscope slide. Other dimensions are also possible. The microscope slide can be a standard microscope slide made of glass. The stainer unitand/or slide can be held at a substantially horizontal orientation. The term “substantially horizontal” generally refers to an angle within about +/−2 degrees of horizontal. In some embodiments, the stainer unitand/or slide are held at about +/−1 degree of horizontal or about +/−0.5 degree of horizontal. The slide can be held at other orientations and positions. The flow cellcan be configured to hold other types of substrates capable of carrying specimens in the form of cytological preparations, micro-arrays, tissue arrays, or the like.

The biological specimens disclosed herein can include one or more biological samples that can be a tissue sample or samples (e.g., any collection of cells) removed from a subject. The tissue sample can be a collection of interconnected cells that perform a similar function within an organism. A biological sample can also be any solid or fluid sample obtained from, excreted by, or secreted by any living organism, including, without limitation, single-celled organisms, such as bacteria, yeast, protozoans, and amoebas, multicellular organisms (e.g., plants or animals, including samples from a healthy or apparently healthy human subject or a human patient affected by a condition or disease to be diagnosed or investigated, such as cancer). In some embodiments, a biological sample is mountable on a microscope slide and includes, without limitation, a section of tissue, an organ, a tumor section, a smear, a frozen section, a cytology prep, or cell lines. An incisional biopsy, a core biopsy, an excisional biopsy, a needle aspiration biopsy, a core needle biopsy, a stereotactic biopsy, an open biopsy, or a surgical biopsy can be used to obtain the sample.

With continued reference to, the dispenser apparatuscan be a robotic pipettor capable of retrieving, preparing, and/or dispensing liquids and can include, without limitation, one or more pipettor heads, aspiration tubes, valves, or other fluidic components. In some embodiments, the dispenser apparatushas a single robotic pipettor configured to process one slide at a time. In other embodiments, the dispenser apparatuscan include a plurality of robotic pipettors for simultaneously processing multiple slides. The number, configurations, and functionality of the robotic pipettors can be selected based on the number of slides to be processed. A mixing station can be part of the stainer unitor a part of the staining instrumentand can serve as a staging area that can significantly increase processing capacity or otherwise enhance processing. Reactive reagents, such as reagents that react immediately upon mixing, can be mixed immediately before dispensing to enhance stain consistency and quality. Because reagents can be staged before they are needed, slide processing capabilities can be increased.

The systems discussed herein can be configured to process non-pipetting stainer units. Such processing systems can include actuators, pushers, pressurizing devices, or other devices capable of operating components of the non-pipetting stainer units. In some embodiments, the end effectorcan press down on blister elements to dispense reagents. In other embodiments, the end effectorcan be in the form a pressurization nozzle configured to output pressurized fluid to cause liquids to flow from reagent reservoirs to the reaction chamber. Layouts and functionality of non-limiting exemplary processing systems are discussed in connection with.

is a block diagram of the systemin accordance with one embodiment of the disclosed technology. The systemcan include an assay processing modulewith a dispenser apparatusthat includes one or more pipettorsand the transporter apparatus. Each pipettercan include one or more positioners(e.g., XYZ positioners) for moving pipettes and fluid components (e.g., valves, fluid lines, etc.) for aspirating and dispensing. The pipettercan acquire tips from a pipette tip storage unitand jettison used tips at a waste area. The systemcan include other dispenser apparatuses in addition to and/or in lieu of the pipettors.

A reader in the form of a barcode readercan acquire information from stainer units, slides, containers or other items with labels or readable information. The information (e.g., consumable ID, tissue information, etc.) can be sent to a controller (e.g., controllerof). The controller can determine a processing protocol based on the received information. Multiple readers can be used to increase throughput. The number, positions, and configurations of the readers can be selected based on target throughput, reading capabilities, or other operating parameters.

The assay processing modulecan include support elements. The support elementscan include one or more processors, sensors, controllers, waste containers, and housing components (e.g., frame, panels, etc.). Controllers can control processing environments, system components and/or communication and can include one or more displays for displaying GUIs or information, for example. Waste containers can store solid waste, such as used pipettor tips. The support elementscan include communication components (e.g., antennae, transmitters, ports, wireless modules, etc.), power supply conditioning/distribution components, or the like. The components and configuration of the support elementscan be selected based on, for example, whether the systemcommunicates with another system or network.

The assay processing modulecan also include one or more control valve modules, clamping modules, consumable locator modules, and/or temperature control modules. The valve control modulescan include one or more sensors (e.g., pressure sensors, temperature sensors, etc.), valves (e.g., one-way valves, diaphragm or membrane valves, etc.), actuators (e.g., pushers for opening/closing diaphragm or membrane valves), and fluid lines, for example. The clamping modulecan clamp onto the stainer unit. For example, the clamping modulecan include a closure device (e.g., closure deviceof) configured to apply pressure to a flow cell, slide, or the like. The consumable locator modulecan physically locate and securely hold consumables. The temperature control modulecan be part of a base (e.g., baseof) and can include one or more thermal elements, insulators, controllers, or the like. Thermal elements can be conduction heaters/coolers, resistive heaters, and/or Peltier devices and can be capable of localized heating/cooling at the flow cell area, so the flow cell and its contents can be heated/cooled without substantially affecting the temperature of the stored reagents.

is a top view of an automated slide processing systemconfigured for parallel processing of stainer units in accordance with an embodiment of the disclosed technology. The systemcan include an array of processing zones or stations(one identified), each capable of holding at least one stainer unit. Each processing stationcan include a station(two separate ones identified) configured to receive cartridges, stainer units, or the like. Although the illustrated embodiment has eight stations, systemcan have any number of stations selected based on the desired processing throughout. Processing areassurround respective stations. A waste reservoir or areacan include a container for collecting solid waste, liquid waste, or both. A supply stationcan include a storage area (e.g., a nested tip rack area, a pipette tip storage area, etc.), coverslips, fluid containers, or the like.

In operation, stainer units can be manually or robotically loaded into the systemvia a feed or input portal(“input portal”). In some embodiments, an interrogation stationhas a detectorpositioned to analyze the slide, stainer units, or both. The detectorcan include one or more readers, optical sensors, cameras, contact sensors, position sensors, or the like. A robotic transporter apparatus can retrieve stainer units from the stationand transport the retrieved stainer units to a desired zone or station. Each specimen-bearing slide can be processed based on one or more signals from the detectoraccording to, for example, one or more arbitrary user-defined sets of operations (e.g., a user-defined staining protocol), pre-defined sets of operations (e.g., preprogrammed protocol), or other processing instructions or routines. Processed stainer units can be parked at an output stationfor removal.

Sensors can be located at various locations throughout processing systems, including on the transporter, within the processing zones, and incorporated into stainer units. In some embodiments, sensors (including, without limitation, strain gauges, accelerometers, contact sensors, optical sensors, or other sensing devices capable of sensing certain events) can be used to detect contact, collisions, impacts, or other events. The sensors can output one or more signals that are received by a controller, which can determine whether a given event requires user notification or other action. For example, if an unexpected position of a cover of a stainer unit is detected, the controller can alert a user to open an access door to visually inspect the stainer unit to determine, for example, whether the slide or cover is positioned properly.